recipe ctat-mutations

Mutation detection in RNA-Seq using GATK-v4.0 in RNA-Seq variant calling, several sources of variant annotation, and filtering based on CRAVAT.

Homepage:

https://github.com/NCIP/ctat-mutations

License:

BSD-3-Clause

Recipe:

/ctat-mutations/meta.yaml

package ctat-mutations

versions:

2.1.0-0,  2.0.1-5,  2.0.1-4,  2.0.1-3,  2.0.1-2,  2.0.1-1,  2.0.1-0,  2.0.0-4,  2.0.0-3, 

2.1.0-0,  2.0.1-5,  2.0.1-4,  2.0.1-3,  2.0.1-2,  2.0.1-1,  2.0.1-0,  2.0.0-4,  2.0.0-3,  2.0.0-0,  1.0-0

depends bcftools:

depends gatk4:

depends openjdk:

>=8

depends picard:

2.18.14.*

depends pysam:

depends python:

>=3.6,<3.7.0a0

depends requests:

2.18.4.*

depends samtools:

depends star:

depends tabix:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install ctat-mutations

and update with::

   mamba update ctat-mutations

To create a new environment, run:

mamba create --name myenvname ctat-mutations

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/ctat-mutations:<tag>

(see `ctat-mutations/tags`_ for valid values for ``<tag>``)

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